## 191 samples selected for analysis
## 191 files found
## All files match a metadata entry.
## All expected files found.
Samples with a PC1 > 2 (the red lines) and/or PC2 zscore > 2.5 (the green lines) were dropped from analysis. Points in red represent samples that were dropped.
## Warning: `arrange_()` is deprecated as of dplyr 0.7.0.
## Please use `arrange()` instead.
## See vignette('programming') for more help
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_warnings()` to see where this warning was generated.
| sample_name | pt_ref | subject_ref | study | subject_id | process_ref | visit_ref | sample_type | visit_date | sample_alias | age | ethnicity | sex | disease_class | reason_group | match_group | random_seed | plate_id | rin | concentration | cell_type | ifc |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| AC027_22 | BPID|023300 | OCRD|1453 | OCRD | 1453 | OCRD|1453|2017-02-24 | OCRD|1453|2017-02-23 | B Cell RNA | 2017-02-23 | S01453-V08702 | 50 | AI | Female | RA | RA-AI | BPID|020101 | 0.0047414 | RNA NARCH_1 | 9.3 | 2.8 | b_cell | IFC1-1970031135 |
| AC060_22 | BPID|013709 | CE|541425 | CE | 541425 | CE|541425|2010-03-29 | CE|541425|2010-03-29 | B Cell RNA | 2010-03-29 | none | 29 | AA | Female | control | CTRL-AA | BPID|023080 | 0.9362812 | RNA NARCH_1 | 8.9 | 2.8 | b_cell | IFC1-1970031135 |
| AC063_32 | BPID|014195 | CE|541936 | CE | 541936 | CE|541936|2010-06-23 | CE|541936|2010-06-22 | T Cell RNA | 2010-06-22 | none | 48 | AA | Female | control | CTRL-AA | BPID|020101 | 0.6564617 | RNA NARCH_2 | 7.9 | 2.8 | t_cell | IFC3-1970031192 |
This MA plot is of shrunken log2 fold changes (using the apeglm package), in which actual fold changes are adjusted to compensate for the high variablity of genes with few counts.
Dots in red indicate a significant expression difference between Control and SLE.
To determine the optimal k, the gap statistic was calculated for k = (3,20) (k = 2 was ignored because it just returns the two disease clusters). A higher coefficient means better intracluster simliarity and intercluster differences.
To determine if there is a gross mixup of samples, examine the expression of sex-specific transcripts to ensure that only female-subject samples express “XIST” and male-subject samples "DDX3Y:
These appear to be correct.
## ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
## setting value
## version R version 4.0.0 (2020-04-24)
## os Ubuntu 18.04.4 LTS
## system x86_64, linux-gnu
## ui X11
## language (EN)
## collate en_US.UTF-8
## ctype en_US.UTF-8
## tz Etc/UTC
## date 2020-10-08
##
## ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
## package * version date lib source
## abind 1.4-5 2016-07-21 [1] RSPM (R 4.0.0)
## acepack 1.4.1 2016-10-29 [1] RSPM (R 4.0.0)
## annotate 1.66.0 2020-04-27 [1] Bioconductor
## AnnotationDbi 1.50.3 2020-07-25 [1] Bioconductor
## assertthat 0.2.1 2019-03-21 [1] RSPM (R 4.0.0)
## backports 1.1.7 2020-05-13 [1] RSPM (R 4.0.0)
## base64enc 0.1-3 2015-07-28 [1] RSPM (R 4.0.0)
## base64url 1.4 2018-05-14 [1] RSPM (R 4.0.0)
## bayesplot 1.7.2 2020-05-28 [1] RSPM (R 4.0.0)
## bibtex 0.4.2.2 2020-01-02 [1] RSPM (R 4.0.0)
## Biobase * 2.48.0 2020-04-27 [1] Bioconductor
## BiocGenerics * 0.34.0 2020-04-27 [1] Bioconductor
## BiocManager * 1.30.10 2019-11-16 [1] CRAN (R 4.0.0)
## BiocParallel * 1.22.0 2020-04-27 [1] Bioconductor
## bit 1.1-15.2 2020-02-10 [1] RSPM (R 4.0.0)
## bit64 0.9-7 2017-05-08 [1] RSPM (R 4.0.0)
## bitops 1.0-6 2013-08-17 [1] RSPM (R 4.0.0)
## blob 1.2.1 2020-01-20 [1] RSPM (R 4.0.0)
## boot 1.3-25 2020-04-26 [2] RSPM (R 4.0.0)
## broom * 0.5.6 2020-04-20 [1] RSPM (R 4.0.0)
## callr 3.4.3 2020-03-28 [1] RSPM (R 4.0.0)
## car 3.0-8 2020-05-21 [1] RSPM (R 4.0.0)
## carData 3.0-4 2020-05-22 [1] RSPM (R 4.0.0)
## caret * 6.0-86 2020-03-20 [1] RSPM (R 4.0.0)
## cellranger 1.1.0 2016-07-27 [1] RSPM (R 4.0.0)
## checkmate 2.0.0 2020-02-06 [1] RSPM (R 4.0.0)
## class 7.3-17 2020-04-26 [2] RSPM (R 4.0.0)
## cli 2.0.2 2020-02-28 [1] RSPM (R 4.0.0)
## cluster * 2.1.0 2019-06-19 [1] RSPM (R 4.0.0)
## clusterProfiler * 3.16.1 2020-08-18 [1] Bioconductor
## codetools 0.2-16 2018-12-24 [2] CRAN (R 4.0.0)
## colorspace 1.4-1 2019-03-18 [1] RSPM (R 4.0.0)
## colourpicker 1.0 2017-09-27 [1] RSPM (R 4.0.0)
## corrplot * 0.84 2017-10-16 [1] RSPM (R 4.0.0)
## cowplot * 1.0.0 2019-07-11 [1] RSPM (R 4.0.0)
## crayon 1.3.4 2017-09-16 [1] RSPM (R 4.0.0)
## crosstalk 1.1.0.1 2020-03-13 [1] RSPM (R 4.0.0)
## curl 4.3 2019-12-02 [1] RSPM (R 4.0.0)
## data.table 1.12.8 2019-12-09 [1] RSPM (R 4.0.0)
## DBI 1.1.0 2019-12-15 [1] RSPM (R 4.0.0)
## dbplyr 1.4.4 2020-05-27 [1] RSPM (R 4.0.0)
## DelayedArray * 0.14.1 2020-07-14 [1] Bioconductor
## DESeq2 * 1.28.1 2020-05-12 [1] Bioconductor
## dials * 0.0.6 2020-04-03 [1] RSPM (R 4.0.0)
## DiceDesign 1.8-1 2019-07-31 [1] RSPM (R 4.0.0)
## digest 0.6.25 2020-02-23 [1] RSPM (R 4.0.0)
## DO.db 2.9 2020-09-18 [1] Bioconductor
## doParallel 1.0.15 2019-08-02 [1] RSPM (R 4.0.0)
## DOSE 3.14.0 2020-04-27 [1] Bioconductor
## downloader 0.4 2015-07-09 [1] RSPM (R 4.0.0)
## dplyr * 1.0.0 2020-05-29 [1] RSPM (R 4.0.0)
## drake * 7.12.2 2020-06-02 [1] RSPM (R 4.0.0)
## DT 0.13 2020-03-23 [1] RSPM (R 4.0.0)
## dygraphs 1.1.1.6 2018-07-11 [1] RSPM (R 4.0.0)
## dynamicTreeCut * 1.63-1 2016-03-11 [1] RSPM (R 4.0.0)
## edgeR 3.30.3 2020-06-02 [1] Bioconductor
## ellipsis 0.3.1 2020-05-15 [1] RSPM (R 4.0.0)
## enrichplot 1.8.1 2020-04-29 [1] Bioconductor
## europepmc 0.4 2020-05-31 [1] RSPM (R 4.0.0)
## evaluate 0.14 2019-05-28 [1] RSPM (R 4.0.0)
## factoextra * 1.0.7 2020-04-01 [1] RSPM (R 4.0.0)
## fansi 0.4.1 2020-01-08 [1] RSPM (R 4.0.0)
## farver 2.0.3 2020-01-16 [1] RSPM (R 4.0.0)
## fastcluster * 1.1.25 2018-06-07 [1] RSPM (R 4.0.0)
## fastmap 1.0.1 2019-10-08 [1] RSPM (R 4.0.0)
## fastmatch 1.1-0 2017-01-28 [1] RSPM (R 4.0.0)
## fgsea 1.14.0 2020-04-27 [1] Bioconductor
## filelock 1.0.2 2018-10-05 [1] RSPM (R 4.0.0)
## flextable * 0.5.10 2020-05-15 [1] RSPM (R 4.0.0)
## forcats * 0.5.0 2020-03-01 [1] RSPM (R 4.0.0)
## foreach 1.5.0 2020-03-30 [1] RSPM (R 4.0.0)
## foreign 0.8-80 2020-05-24 [2] RSPM (R 4.0.0)
## formattable * 0.2.0.1 2016-08-05 [1] RSPM (R 4.0.0)
## Formula 1.2-3 2018-05-03 [1] RSPM (R 4.0.0)
## fs 1.4.1 2020-04-04 [1] RSPM (R 4.0.0)
## furrr * 0.1.0 2018-05-16 [1] RSPM (R 4.0.0)
## future * 1.17.0 2020-04-18 [1] RSPM (R 4.0.0)
## gdtools 0.2.2 2020-04-03 [1] RSPM (R 4.0.0)
## genefilter * 1.70.0 2020-04-27 [1] Bioconductor
## geneplotter 1.66.0 2020-04-27 [1] Bioconductor
## generics 0.0.2 2018-11-29 [1] RSPM (R 4.0.0)
## GenomeInfoDb * 1.24.2 2020-06-15 [1] Bioconductor
## GenomeInfoDbData 1.2.3 2020-09-18 [1] Bioconductor
## GenomicRanges * 1.40.0 2020-04-27 [1] Bioconductor
## ggfittext 0.8.1 2019-07-18 [1] RSPM (R 4.0.0)
## ggforce * 0.3.1 2019-08-20 [1] RSPM (R 4.0.0)
## ggplot2 * 3.3.1 2020-05-28 [1] RSPM (R 4.0.0)
## ggplotify * 0.0.5 2020-03-12 [1] RSPM (R 4.0.0)
## ggpubr * 0.3.0 2020-05-04 [1] RSPM (R 4.0.0)
## ggradar * 0.2 2020-09-18 [1] Github (ricardo-bion/ggradar@63e5cef)
## ggraph 2.0.3 2020-05-20 [1] RSPM (R 4.0.0)
## ggrepel * 0.8.2 2020-03-08 [1] RSPM (R 4.0.0)
## ggridges 0.5.2 2020-01-12 [1] RSPM (R 4.0.0)
## ggsignif 0.6.0 2019-08-08 [1] RSPM (R 4.0.0)
## ggtext * 0.1.0 2020-06-04 [1] RSPM (R 4.0.0)
## globals 0.12.5 2019-12-07 [1] RSPM (R 4.0.0)
## glue 1.4.1 2020-05-13 [1] RSPM (R 4.0.0)
## GO.db 3.11.4 2020-09-18 [1] Bioconductor
## GOSemSim 2.14.2 2020-09-04 [1] Bioconductor
## gower 0.2.1 2019-05-14 [1] RSPM (R 4.0.0)
## GPfit 1.0-8 2019-02-08 [1] RSPM (R 4.0.0)
## graphlayouts 0.7.0 2020-04-25 [1] RSPM (R 4.0.0)
## gridBase 0.4-7 2014-02-24 [1] RSPM (R 4.0.0)
## gridExtra 2.3 2017-09-09 [1] RSPM (R 4.0.0)
## gridGraphics 0.5-0 2020-02-25 [1] RSPM (R 4.0.0)
## gridtext 0.1.1 2020-02-24 [1] RSPM (R 4.0.0)
## gtable 0.3.0 2019-03-25 [1] RSPM (R 4.0.0)
## gtools * 3.8.2 2020-03-31 [1] RSPM (R 4.0.0)
## haven 2.3.1 2020-06-01 [1] RSPM (R 4.0.0)
## HGNChelper * 0.8.1 2019-10-24 [1] RSPM (R 4.0.0)
## highr 0.8 2019-03-20 [1] RSPM (R 4.0.0)
## Hmisc 4.4-0 2020-03-23 [1] RSPM (R 4.0.0)
## hms 0.5.3 2020-01-08 [1] RSPM (R 4.0.0)
## htmlTable 1.13.3 2019-12-04 [1] RSPM (R 4.0.0)
## htmltools 0.4.0 2019-10-04 [1] RSPM (R 4.0.0)
## htmlwidgets 1.5.1 2019-10-08 [1] RSPM (R 4.0.0)
## httpuv 1.5.4 2020-06-06 [1] RSPM (R 4.0.0)
## httr 1.4.1 2019-08-05 [1] RSPM (R 4.0.0)
## igraph 1.2.5 2020-03-19 [1] RSPM (R 4.0.0)
## impute 1.62.0 2020-04-27 [1] Bioconductor
## infer * 0.5.1 2019-11-19 [1] RSPM (R 4.0.0)
## inline 0.3.15 2018-05-18 [1] RSPM (R 4.0.0)
## inspectdf 0.0.7 2019-11-05 [1] RSPM (R 4.0.0)
## ipred 0.9-9 2019-04-28 [1] RSPM (R 4.0.0)
## IRanges * 2.22.2 2020-05-21 [1] Bioconductor
## irlba 2.3.3 2019-02-05 [1] RSPM (R 4.0.0)
## iterators 1.0.12 2019-07-26 [1] RSPM (R 4.0.0)
## janeaustenr 0.1.5 2017-06-10 [1] RSPM (R 4.0.0)
## janitor * 2.0.1 2020-04-12 [1] RSPM (R 4.0.0)
## jpeg 0.1-8.1 2019-10-24 [1] RSPM (R 4.0.0)
## jsonlite 1.6.1 2020-02-02 [1] RSPM (R 4.0.0)
## kableExtra * 1.1.0 2019-03-16 [1] RSPM (R 4.0.0)
## knitr 1.28 2020-02-06 [1] RSPM (R 4.0.0)
## labeling 0.3 2014-08-23 [1] RSPM (R 4.0.0)
## later 1.1.0.1 2020-06-05 [1] RSPM (R 4.0.0)
## lattice * 0.20-41 2020-04-02 [2] CRAN (R 4.0.0)
## latticeExtra 0.6-29 2019-12-19 [1] RSPM (R 4.0.0)
## lava 1.6.7 2020-03-05 [1] RSPM (R 4.0.0)
## lazyeval 0.2.2 2019-03-15 [1] RSPM (R 4.0.0)
## lhs 1.0.2 2020-04-13 [1] RSPM (R 4.0.0)
## lifecycle 0.2.0 2020-03-06 [1] RSPM (R 4.0.0)
## limma 3.44.3 2020-06-12 [1] Bioconductor
## listenv 0.8.0 2019-12-05 [1] RSPM (R 4.0.0)
## lme4 1.1-23 2020-04-07 [1] RSPM (R 4.0.0)
## locfit 1.5-9.4 2020-03-25 [1] RSPM (R 4.0.0)
## loo 2.2.0 2019-12-19 [1] RSPM (R 4.0.0)
## lubridate 1.7.8 2020-04-06 [1] RSPM (R 4.0.0)
## magrittr 1.5 2014-11-22 [1] RSPM (R 4.0.0)
## markdown 1.1 2019-08-07 [1] RSPM (R 4.0.0)
## MASS 7.3-51.6 2020-04-26 [2] RSPM (R 4.0.0)
## Matrix * 1.2-18 2019-11-27 [2] CRAN (R 4.0.0)
## matrixStats * 0.56.0 2020-03-13 [1] RSPM (R 4.0.0)
## memoise 1.1.0 2017-04-21 [1] RSPM (R 4.0.0)
## mgcv * 1.8-31 2019-11-09 [2] CRAN (R 4.0.0)
## mime 0.9 2020-02-04 [1] RSPM (R 4.0.0)
## miniUI 0.1.1.1 2018-05-18 [1] RSPM (R 4.0.0)
## minqa 1.2.4 2014-10-09 [1] RSPM (R 4.0.0)
## ModelMetrics 1.2.2.2 2020-03-17 [1] RSPM (R 4.0.0)
## modelr 0.1.8 2020-05-19 [1] RSPM (R 4.0.0)
## moduleScoreR * 0.0.0.9200 2020-09-18 [1] Github (milescsmith/moduleScoreR@e6db70f)
## munsell 0.5.0 2018-06-12 [1] RSPM (R 4.0.0)
## nlme * 3.1-148 2020-05-24 [2] RSPM (R 4.0.0)
## nloptr 1.2.2.1 2020-03-11 [1] RSPM (R 4.0.0)
## NMF 0.22.0 2020-02-12 [1] RSPM (R 4.0.0)
## nnet 7.3-14 2020-04-26 [2] RSPM (R 4.0.0)
## officer 0.3.11 2020-05-18 [1] RSPM (R 4.0.0)
## openxlsx 4.1.5 2020-05-06 [1] RSPM (R 4.0.0)
## paletteer * 1.2.0 2020-06-07 [1] RSPM (R 4.0.0)
## parsnip * 0.1.1 2020-05-06 [1] RSPM (R 4.0.0)
## pheatmap * 1.0.12 2019-01-04 [1] RSPM (R 4.0.0)
## pillar 1.4.4 2020-05-05 [1] RSPM (R 4.0.0)
## pkgbuild 1.0.8 2020-05-07 [1] RSPM (R 4.0.0)
## pkgconfig 2.0.3 2019-09-22 [1] RSPM (R 4.0.0)
## pkgmaker 0.31.1 2020-03-19 [1] RSPM (R 4.0.0)
## plotly * 4.9.2.1 2020-04-04 [1] RSPM (R 4.0.0)
## plyr 1.8.6 2020-03-03 [1] RSPM (R 4.0.0)
## png 0.1-7 2013-12-03 [1] RSPM (R 4.0.0)
## polyclip 1.10-0 2019-03-14 [1] RSPM (R 4.0.0)
## preprocessCore 1.50.0 2020-04-27 [1] Bioconductor
## prettyunits 1.1.1 2020-01-24 [1] RSPM (R 4.0.0)
## pROC 1.16.2 2020-03-19 [1] RSPM (R 4.0.0)
## processx 3.4.2 2020-02-09 [1] RSPM (R 4.0.0)
## prodlim 2019.11.13 2019-11-17 [1] RSPM (R 4.0.0)
## progress 1.2.2 2019-05-16 [1] RSPM (R 4.0.0)
## promises 1.1.0 2019-10-04 [1] RSPM (R 4.0.0)
## ps 1.3.3 2020-05-08 [1] RSPM (R 4.0.0)
## purrr * 0.3.4 2020-04-17 [1] RSPM (R 4.0.0)
## qvalue 2.20.0 2020-04-27 [1] Bioconductor
## R6 2.4.1 2019-11-12 [1] RSPM (R 4.0.0)
## randomForest * 4.6-14 2018-03-25 [1] RSPM (R 4.0.0)
## RColorBrewer * 1.1-2 2014-12-07 [1] RSPM (R 4.0.0)
## Rcpp 1.0.4.6 2020-04-09 [1] RSPM (R 4.0.0)
## RCurl 1.98-1.2 2020-04-18 [1] RSPM (R 4.0.0)
## readr * 1.3.1 2018-12-21 [1] RSPM (R 4.0.0)
## readxl * 1.3.1 2019-03-13 [1] RSPM (R 4.0.0)
## recipes * 0.1.12 2020-05-01 [1] RSPM (R 4.0.0)
## registry 0.5-1 2019-03-05 [1] RSPM (R 4.0.0)
## rematch2 2.1.2 2020-05-01 [1] RSPM (R 4.0.0)
## reprex 0.3.0 2019-05-16 [1] RSPM (R 4.0.0)
## reshape2 1.4.4 2020-04-09 [1] RSPM (R 4.0.0)
## rio 0.5.16 2018-11-26 [1] RSPM (R 4.0.0)
## rlang * 0.4.6 2020-05-02 [1] RSPM (R 4.0.0)
## rmarkdown 2.2 2020-05-31 [1] RSPM (R 4.0.0)
## rngtools 1.5 2020-01-23 [1] RSPM (R 4.0.0)
## rpart 4.1-15 2019-04-12 [2] CRAN (R 4.0.0)
## rsample * 0.0.7 2020-06-04 [1] RSPM (R 4.0.0)
## rsconnect 0.8.16 2019-12-13 [1] RSPM (R 4.0.0)
## RSQLite 2.2.0 2020-01-07 [1] RSPM (R 4.0.0)
## rstan 2.19.3 2020-02-11 [1] RSPM (R 4.0.0)
## rstanarm 2.19.3 2020-02-11 [1] RSPM (R 4.0.0)
## rstantools 2.1.0 2020-06-01 [1] RSPM (R 4.0.0)
## rstatix * 0.6.0.999 2020-09-18 [1] Github (milescsmith/rstatix@6f5e0a6)
## rstudioapi 0.11 2020-02-07 [1] RSPM (R 4.0.0)
## rsvd 1.0.3 2020-02-17 [1] RSPM (R 4.0.0)
## rvcheck 0.1.8 2020-03-01 [1] RSPM (R 4.0.0)
## rvest 0.3.5 2019-11-08 [1] RSPM (R 4.0.0)
## S4Vectors * 0.26.1 2020-05-16 [1] Bioconductor
## scales * 1.1.1 2020-05-11 [1] RSPM (R 4.0.0)
## scatterpie 0.1.4 2019-11-08 [1] RSPM (R 4.0.0)
## sessioninfo 1.1.1 2018-11-05 [1] RSPM (R 4.0.0)
## shiny 1.4.0.2 2020-03-13 [1] RSPM (R 4.0.0)
## shinyjs 1.1 2020-01-13 [1] RSPM (R 4.0.0)
## shinystan 2.5.0 2018-05-01 [1] RSPM (R 4.0.0)
## shinythemes 1.1.2 2018-11-06 [1] RSPM (R 4.0.0)
## snakecase 0.11.0 2019-05-25 [1] RSPM (R 4.0.0)
## SnowballC 0.7.0 2020-04-01 [1] RSPM (R 4.0.0)
## StanHeaders 2.21.0-3 2020-05-28 [1] RSPM (R 4.0.0)
## statmod 1.4.34 2020-02-17 [1] RSPM (R 4.0.0)
## storr 1.2.1 2018-10-18 [1] RSPM (R 4.0.0)
## stringi 1.4.6 2020-02-17 [1] RSPM (R 4.0.0)
## stringr * 1.4.0 2019-02-10 [1] RSPM (R 4.0.0)
## SummarizedExperiment * 1.18.2 2020-07-09 [1] Bioconductor
## survival 3.1-12 2020-04-10 [2] CRAN (R 4.0.0)
## sva * 3.36.0 2020-04-27 [1] Bioconductor
## systemfonts 0.2.2 2020-05-14 [1] RSPM (R 4.0.0)
## threejs 0.3.3 2020-01-21 [1] RSPM (R 4.0.0)
## tibble * 3.0.1 2020-04-20 [1] RSPM (R 4.0.0)
## tidygraph 1.2.0 2020-05-12 [1] RSPM (R 4.0.0)
## tidymodels * 0.1.0 2020-02-16 [1] RSPM (R 4.0.0)
## tidyposterior 0.0.2 2018-11-15 [1] RSPM (R 4.0.0)
## tidypredict 0.4.5 2020-02-10 [1] RSPM (R 4.0.0)
## tidyr * 1.1.0 2020-05-20 [1] RSPM (R 4.0.0)
## tidyselect * 1.1.0 2020-05-11 [1] RSPM (R 4.0.0)
## tidytext 0.2.4 2020-04-17 [1] RSPM (R 4.0.0)
## tidyverse * 1.3.0 2019-11-21 [1] RSPM (R 4.0.0)
## timeDate 3043.102 2018-02-21 [1] RSPM (R 4.0.0)
## tokenizers 0.2.1 2018-03-29 [1] RSPM (R 4.0.0)
## triebeard 0.3.0 2016-08-04 [1] RSPM (R 4.0.0)
## tune * 0.1.0 2020-04-02 [1] RSPM (R 4.0.0)
## tweenr 1.0.1 2018-12-14 [1] RSPM (R 4.0.0)
## tximport * 1.16.1 2020-06-05 [1] Bioconductor
## txtq 0.2.0 2019-10-15 [1] RSPM (R 4.0.0)
## urltools 1.7.3 2019-04-14 [1] RSPM (R 4.0.0)
## uuid 0.1-4 2020-02-26 [1] RSPM (R 4.0.0)
## uwot * 0.1.8 2020-03-16 [1] RSPM (R 4.0.0)
## vctrs 0.3.1 2020-06-05 [1] RSPM (R 4.0.0)
## viridis * 0.5.1 2018-03-29 [1] RSPM (R 4.0.0)
## viridisLite * 0.3.0 2018-02-01 [1] RSPM (R 4.0.0)
## webshot 0.5.2 2019-11-22 [1] RSPM (R 4.0.0)
## WGCNA * 1.69 2020-02-28 [1] RSPM (R 4.0.0)
## withr 2.2.0 2020-04-20 [1] RSPM (R 4.0.0)
## workflows * 0.1.1 2020-03-17 [1] RSPM (R 4.0.0)
## xfun 0.14 2020-05-20 [1] RSPM (R 4.0.0)
## XML 3.99-0.3 2020-01-20 [1] RSPM (R 4.0.0)
## xml2 1.3.2 2020-04-23 [1] RSPM (R 4.0.0)
## xtable 1.8-4 2019-04-21 [1] RSPM (R 4.0.0)
## xts 0.12-0 2020-01-19 [1] RSPM (R 4.0.0)
## XVector 0.28.0 2020-04-27 [1] Bioconductor
## yaml 2.2.1 2020-02-01 [1] RSPM (R 4.0.0)
## yardstick * 0.0.6 2020-03-17 [1] RSPM (R 4.0.0)
## zip 2.0.4 2019-09-01 [1] RSPM (R 4.0.0)
## zlibbioc 1.34.0 2020-04-27 [1] Bioconductor
## zoo 1.8-8 2020-05-02 [1] RSPM (R 4.0.0)
##
## [1] /usr/local/lib/R/site-library
## [2] /usr/local/lib/R/library